Mass Spectrometry-Based Methods for
Protein Identification
Joseph A. Loo
Department of Biological Chemistry
David Geffen School of Medicine
Department of Chemistry and
Biochemistry
University of California
Los Angeles, CA USA
Genomics and Proteomics
Characterizing many genes and gene products simultaneously
Proteomics Aids Biological Research
complex
protein
mixture
Biology
protein separation
mass spectrometry
protein identification
protein modification
protein abundance
Proteomics - What is it?
 An assay to systematically analyze the diverse
properties of proteins
 Biological processes are dynamic
 A quantitative comparison of states is required
 The study of protein expression and function on a
genome scale
 Purpose: Examine altered gene expression pathways
in disease states and under different environmental
conditions
The completion of the human genome has
provided researchers with the blueprint for life,
and proteomics offers scientists the means for
analyzing the expressed genome.
Genome to Proteome
dsDNA
(Gene)
Transcription
mRNA
Translation
H2N
COOH
Protein
MTDLKASSLRALKLMDLTTLNDDDTDEKVIALCHQAKTPVGNTAAICIYP
51 RFIPIARKTLKEQGTPEIRIATVTNFPHGNDDIDIALAETRAAIAYGADE
101 VDVVFPYRALMAGNEQVGFDLVKACKEACAAANVLLKVIIETGELKDEAL
151 IRKASEISI
Mass spectrometry
The completion of the human genome has
provided researchers with the blueprint for
life, and proteomics offers scientists the
means for analyzing the expressed genome.
Approaches for Protein Identification
What is this
protein?
 Molecular weight
 Isoelectric point
 Amino acid composition
 Other physical/chemical characteristics
 Partial or complete amino acid sequence



Edman (N-terminal sequence) - if N-term. not blocked
C-terminal sequence - not commonly performed
Mass spectrometry-measured information
Protein Identification by Mass Spectrometry
MW x 103
2-D Gel Electrophoresis
1507540-
Excise
separated
protein
“spots”
2518106.5
6.0
5.5
5.0
4.5
pI
In-gel
trypsin
digest
1547
Peptide mass fingerprint by
MALDI-TOF or LC-ESI-MS.
Additional sequence
information can be obtained by
MS/MS.
717
1089
1272
1401
2384
1857
1700
Recover
tryptic
peptides
2791
500
2500
1500
m/z
Protein identification by searching
proteomic or genomic databases
3000
Mass Spectrometry:
A method to “weigh” molecules
Other information can be inferred from a
weight measurement.
 Post-translational
modifications
 Molecular interactions
 Shape
 Sequence
 Physical dimensions
 etc...
A simple measurement of
mass is used to confirm the
identity of a molecule, but it
can be used for much
more……
Mass Spectrometer
for Proteomics
Pre-Separation
Ion Source
Liquid Chromatography
Mass Analyzer
Ion
Detector
Time-of-Flight (TOF)
Quadrupole TOF (QTOF)
Ion Trap (IT)
Fourier TransformIon Cyclotron Resonance (FT-ICR)
The Nobel Prize in Chemistry 2002
"for the development of methods for identification and
structure analyses of biological macromolecules"
"for their development of soft desorption ionisation
methods for mass spectrometric analyses of biological
macromolecules"
John Fenn
Koichi Tanaka
Electrospray: Generation of aerosols and droplets
Electrospray Ionization (ESI)
ESI
MS
highly charge
droplets
 MW range > 150 kDa
20+
19+
18+
21+
17+
16+
22+
15+
500
700
900
 Multiple charging
 More charges for larger
molecules
14+
1100
mass/charge (m/z)
 Liquid introduction of analyte
 Interface with liquid
separation methods, e.g.
liquid chromatography
 Tandem mass spectrometry
(MS/MS) for protein
sequencing
IGF 1R, fraction 1
Operator: JL
Conditions: NH4bicarb
Instrument: Q-TOF
Collision Energy: 4
ESI-MS of Large100Proteins
46512
distribution of multiply charged molecules
1R, fraction 1
rator: JL
ditions: NH4bicarb
Instrument: Q-TOF
Collision Energy: 4
100
(M+15H)15+
3102
9-JUL-2001
Laboratory: PGRD - Discovery Technologies
Cone (V): 150
(M+14H)14+
3323
46048
%
(M+13H)13+
%
3543
(M+16H)16+
0
45000
46000
47000
mass
0
2750
3000
3250
m/z
3500
3750
4000
ESI-MS (Q-TOF)
pH 7.5
m/z
48
History of Electrospray Ionization
 Malcolm Dole demonstrated the production of intact oligomers of
polystyrene up to MW 500,000
 mass analysis of large ions was problematic
 John Fenn (Yale University)
 Chemical engineer - expert in supersonic molecular beams
 Began work on electrospray in 1981
 Adapted ESI to operate on a more “conventional” mass
spectrometer
 Recognized that multiply charged ions were produced by ESI
 Reduced the m/z range required
Electrospray process
Cathode
+
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106 charges for 30
micron droplet
_
+
Power Supply
 Analyte dissolved in a suitable solvent flows
through a small diameter capillary tube
 Liquid in the presence of a high electric field
generates a fine “mist” or aerosol spray of highly
charged droplets
Matrix-assisted Laser
Desorption/Ionization (MALDI)
Time-of-Flight (TOF) Analyzer
detector
high voltage
v3
m3
MALDI
v2
m2
v1
m1
sample
laser
drift region
m1
m2
m3
MALDI Mass Spectrometry of Large
Proteins
100
97430
MALDI-MS of rat MVP
% Intensity
(M+H)+
98563
(M+2H)2+
48658
36446
58309
30811
50608
70405
90202
m/z
110000
129797
MALDI
sample
and
matrix
 Developed by Tanaka (Japan) and
pulsed
laser light
peptide/protein ions
desorbed from matrix
20 kV
(sample stage or target)
Hillenkamp/Karas (Germany)
 Peptide/protein analyte of interest is
co-crystallized on the MALDI target
plate with an appropriate matrix
 small, highly conjugated organic
molecules which strongly absorb
energy at a particular wavelength
 Energy is transferred to analyte
indirectly, inducing desorption
from target surface
 Analyte is ionized by gas-phase
proton transfer (perhaps from
ionized matrix molecules)
MALDI matrices
O
OH
O
O
OH
OH
OH
N
HO
OMe
MeO
OH
OH
4-hydroxy-cyanocinnamic
acid (“alphacyano” or 4HCCA)
peptides
2,5-dihydroxybenzoic acid (DHB)
peptides and proteins
matrices for 337 nm irradiation
3,5-dimethoxy-4hydroxycinnamic
acid (sinapinic acid)
proteins
MALDI
 337 nm irradiation is provided by
a nitrogen (N2) laser
 The target plate is inserted into
the high vacuum region of the
source and the sample is
irradiated with a laser pulse. The
matrix absorbs the laser energy
and transfers energy to the
analyte molecule. The
molecules are desorbed and
ionized during this stage of the
process.
 MALDI is most commonly
interfaced to a time-of-flight
(TOF) mass spectrometer.
R. Aebersold and M. Mann, Nature (2003), 422, 198-207.
Time-of-Flight Mass Spectrometer
v3
m3
v2
m2
v1
m1
detector
drift region
(L)
high voltage
Principal of Operation of Linear TOF
A time-of-flight mass spectrometer measures the mass-dependent time it takes ions of different masses
to move from the ion source to the detector. This requires that the starting time (the time at which the ions
leave the ion source) is well-defined. Recall that the kinetic energy of an ion is:
where “” is ion velocity, “m” is mass, “e” is charge on electron, and “V” is
electric field.
The ion velocity, , is also the length of the flight path, L , divided by the flight time, t:
Substituting this expression for  into the kinetic energy relation, we can derive the working equation for the
time-of-flight mass spectrometer:
mass is proportional to (time)2
Approaches for Protein Sequencing and
Identification
“Top Down”
MS/MS
MIRERICACVLALGMLTGFTHAFGSKDAAADGKPLVVTTIGMIADAVKNIAQGDVHLKGLMGP
GVDPHLYTATAGDVEWLGNADLILYNGLHLETKMGEVFSKLRGSRLVVAVSETIPVSQRLSLE
EAEFDPHVWFDVKLWSYSVKAVYESLCKLLPGKTREFTQRYQAYQQQLDKLDAYVRRKAQS
LPAERRVLVTAHDAFGYFSRAYGFEVKGLQGVSTASEASAHDMQELAAFIAQRKLPAIFIESSI
PHKNVEALRDAVQARGHVVQIGGELFSDAMGDAGTSEGTYVGMVTHNIDTIVAALAR
Enzymatic or
chemical
degradation
MS/MS
“Bottom Up”
Identification of proteins from gels
 Proteins are separated first by high resolution two-dimensional
polyacrylamide gel electrophoresis and then stained. At this point,
to identify an individual or set of protein spots, several options can
be considered by the researcher, depending on availability of
techniques.
 For protein spots that appear to be relatively abundant (e.g.,
more than 1 pmol), traditional protein characterization methods
may be employed.
 Methods such as amino acid analysis and Edman
sequencing can be used to provide necessary protein
identification information. With 2-DE, approximate
molecular weight and isoelectric point characteristics are
provided. Augmented with information on amino acid
composition and/or amino-terminal sequence, a confident
identification can be obtained.
 The sensitivity gains of using MS allows for the identification of
proteins below the one pmol level and in many cases in the
femtomole regime.
Protein Identification by Mass Spectrometry
MW x 103
2-D Gel Electrophoresis
1507540-
Excise
separated
protein
“spots”
2518106.5
6.0
5.5
5.0
4.5
pI
In-gel
trypsin
digest
1547
Peptide mass fingerprint by
MALDI-TOF or LC-ESI-MS.
Additional sequence
information can be obtained by
MS/MS.
717
1089
1272
1401
2384
1857
1700
Recover
tryptic
peptides
2791
500
2500
1500
m/z
Protein identification by searching
proteomic or genomic databases
3000
Protein Cleavage
 For the application of mass
spectrometry for protein
identification, the protein
bands/spots from a 2-D gel are
excised and are exposed to a
highly specific enzymatic cleavage
reagent (e.g., trypsin cleaves on
the C-terminal side of arginine and
lysine residues). The resulting
tryptic fragments are extracted
from the gel slice and are then
subjected to MS-methods. One of
the major barriers to high
throughput in the proteomic
approach to protein identification is
the “in-gel” proteolytic digestion
and subsequent extraction of the
proteolytic peptides from the gel.
Common protocols for this process
are often long and labor intensive.
protein digestion robot
Protein cleavage - proteolysis and
chemical methods
Enzyme and chemical cleavage
reagents
trypsin
endoproteinase Lys-C
endoproteinase Arg-C
endoproteinase Glu-C (V8 protease)
chymotrypsin
elastase
pepsin
Asp-N
thermolysin
carboxypeptidase A/Y
mild acid
cyanogen bromide (CNBr)
BNPS-skatole
PNGase F
alkaline phosphatase
Cleavage sites, comments
C-terminal to R and K (except R-P, K-P bond); R-K, K-K, R-R,
K-R cleave slower
C-terminal to K (rarely K-P bond)
C-terminal to R (except R-P bond)
C-terminal to E and D (except C-P, D-P bond)
C-terminal to F, Y, W, L, I, V, M (except X-P bond)
C-terminal to G, A, S, V, L, I (not very specific)
C-terminal to F, L, E (pH 2-4 active range)
N-terminal to D (sometimes E)
N-terminal to L/, I, V, F (and others to a lesser extent)
cleaves C-terminal residues
cleaves D-P bond
C-terminus of M; M-T and M-S cleave slower; oxidized M do
not cleave
cleaves W-X bond
cleaves N-linked (Asn-glyco) glycoproteins; leaves entire
carbohydrate portion intact and converts N to D
dephosphorylation of phosphoproteins
Mass spectrometry-based protein
identification
 A mass spectrum of the resulting digest products produces a “peptide
map” or a “peptide fingerprint”.
 The measured masses can be compared to theoretical peptide
maps derived from database sequences for identification. There
are a few choices of mass analysis that can be selected from this
point, depending on available instrumentation and other factors.
The resulting peptide fragments can be subjected to MALDI-MS or
ESI-MS analysis.
 A small aliquot of the digest solution can be directly analyzed by
MALDI-MS to obtain a peptide map. The resulting sequence
coverage (relative to the entire protein sequence) displayed from the
total number of tryptic peptides observed in the MALDI mass
spectrum can be quite high, i.e., greater than 80% of the sequence,
although it can vary considerably depending on the protein, sample
amount, etc. The measured molecular weights of the peptide
fragments along with the specificity of the enzyme employed can be
searched and compared against protein sequence databases using a
number of computer searching routines available on the Internet.
Protein identification from peptide
fragments
Protein
Tryptic peptides
Mass spectrum
Protein
sequence
Theoretical
tryptic peptides
Theoretical
mass spectrum
SEMHIKHYTTKILGFRE
EGDSCPLKQWDDSKIL
VAVADKLLEYEEKILLF
NSAKYLLDESSTYKLM
HDDSV
SEMHIKHYTTK
ILGFR
EEGDSCPLK
QWDDSK
ILVAVADK
LLEYEEK
ILLFNSAK
YLLDESSTYK
LMHDDSV
1247.70
ARIIVVTSGK
CERRVVYDFV
VAKVLDDLKA
DSDRILGILA
ILRIKLVGVI
PFRFIEEEKK
1500
GGVGKTTSSA
NVIQGDATLN
MDFEFIVCDS
SKSRRAENGE
PEDQSVLRAS
GFLKRLFGG
2000
AIATGLAQKG
QALIKDKRTE
PAGIETGALM
EPIKEHLLLT
NQGEPVILDI
2719.48
*
2550.52
*
2476.21
2005.07
1849.12
1811.85
1665.89
*trypsin autolysis
1574.20
1424.85
1287.73
1000
1505.77
all peaks are (M+H)+
1375.76
1116.67
MALDI-MS of tryptic peptides
2500
3000
KKTVVIDFDI
NLYILPASQT
ALYFADEAII
RYNPGRVSRG
NADAGKAYAD
GLRNLDLIMG
RDKDALTREG
TTNPEVSSVR
DMLSMEDVLE
TVERLLGER
m/z
ESI-MS and LC-MS for protein identification
 An approach for peptide mapping similar to MALDI-MS uses ESI-MS. A peptide
map can be obtained by analysis of the peptide mixture by ESI-MS. An
advantage of ESI is its ease of coupling to separation methodologies such as
HPLC. Thus, alternatively, to reduce the complexity of the mixture, the peptides
can be separated by HPLC with subsequent mass measurement by on-line ESIMS. The measured masses can be compared to sequence databases.
100
Rel. Abund.
9.4
8.4
6.8
7.7
8.9
8
9
9.8
LC-MS
with ESI
6.2
0
Rel. Abund.
100
5
6
7
10 11 12 Time (min)
965.3
(M+2H)2+
MW ~ 1928.6 Da
629.0
0
400
800
1200
1600
2000
m/z
LC-MS/MS for protein identification
 An improvement in throughput of the overall method can be obtained by
performing LC-MS/MS in the data dependant mode. As full scan mass spectra
are acquired continuously in LC-MS mode, any ion detected with a signal
intensity above a pre-defined threshold will trigger the mass spectrometer to
switch over to MS/MS mode. Thus, the mass spectrometer switches back and
forth between MS- (molecular mass information) and MS/MS mode (sequence
information) in a single LC run. The data dependant scanning capability can
dramatically increase the capacity and throughput for protein identification.
9.4
8.4
9.8
LC-MS
y12
1261.4
LC-MS/MS
y10
6.8
5 6 7 8 9 10 11 12Time (min)
965.3
(M+2H)2+
MS/MS
629.0
b3
y4
b6
668.4 b8
b5 838.5 y9
y8
y13
1374.5
y11
y14
1474.4
400 600 800 1000 1200 1400 1600 1800
400
800 1200 1600 2000 m/z
m/z
Peptide sequencing by mass spectrometry
N-term.
A
B
C
E
D
C-term.
 Peptide molecules are fragmented by collisionally activated dissociation
(CAD)
 collisions with neutral background gas molecules (nitrogen, argon, etc)
 typically dissociate by cleavage of -CO-NH- bond
A
A
A
B
A
B
N-terminal
product ions
m/z
C
B
C
D
A
B
C
D
E
Peptide sequencing by mass spectrometry
 Ideally, one can measure the spacings between product ion peaks to deduce
the sequence
 if each amide bond dissociates with equal probability
 if only a single amide bond fragments for each molecule
 if only C-terminal or N-terminal products ions are formed
 In reality, this is not the case…
D
E
E
B
C
C-terminal
product ions
m/z
D
C
E
D
A
E
B
C
D
E
Nomenclature for MS Sequencing of Peptides
Klaus Biemann, MIT
subscript denotes the number of
residues contained in product ion
N-terminal fragments
b2
b1
R1 O
b3
R2 O
R3 O
R4
H2N - C - C - N - C - C - N - C - C - N - C - COOH
H
H
y3
H
H
y2
C-terminal fragments
H
H
y1
H
Nomenclature for MS Sequencing of Peptides
 Low-energy collisions promote fragmentation of a peptide primarily




along the peptide backbone
Peptide fragmentation which maintains the charge on the C terminus is
designated a y-ion
Fragmentation which maintains the charge on the N terminus is
designated a b-ion
Low energy collisions: ion trap, QQQ, QTOF, FT-ICR
High energy collisions: TOF-TOF
 cleavage of amino acid side chain bonds (d-ion and w-ion)
 differentiate Leu vs. Ile
Peptide Sequencing by Mass Spectrometry
y4-14
242
LVDKVIGITNEEAISTAR
b3-17
100
Rel. Abund.
y12
1261.4
y10
mixture of b-ions and yions are present
Cysteine Synthase A
259
1091.5
y13
1374.5
MS/MS of 2+ charged
tryptic peptides yield
(often) 1+ charged
product ions (but 2+
charged products can
be observed as well)
b6
b5
b3
0
668.4
555.4
y 4 b y5
4
y6
400
600
b8
y9
838.5
990.5
b7
y7
800
y8 b9
b10
1000
y14
y11
b11
1200
b12
1474.4
b14
b
13
1400
b15 b16 b17
1600
1800
m/z
Computer-based Sequence Searching
Strategies
 A list of experimentally determined masses is compared to lists
of computer-generated theoretical masses prepared from a
database of protein primary sequences. With the current
exponential growth in the generation of genomic data, these
databases are expanding every day.
 There are typically three types of search strategies employed:
 searching with peptide fingerprint data
 searching with sequence data
 searching with raw MS/MS data.
 One limiting factor that must be considered for all of the
approaches is that they can only identify proteins that have been
identified and reside within an available database, or very
homologous to one that resides in the database.
Searching with Peptide Fingerprints
 The majority of the available search engines allow
one to define certain experimental parameters to
optimize a particular search.
 Minimum number of peptides to be matched
 Allowable mass error
 Monoisotopic versus average mass data
 Mass range of starting protein
 Type of protease used for digestion
 Information about potential protein modification,
such as N- and C-terminal modification,
carboxymethylation, oxidized methionines, etc.
Searching with Peptide Fingerprints



Most protein databases contain primary sequence
information only
 Any shift in mass incorporated into the primary
sequence as a result of post-translational
modification will result in an experimental mass
that is in disagreement with the theoretical mass.
Modifications such as glycation and phosphorylation
can result in missed identifications.
A single amino acid substitution can shift the mass
of a peptide to such a degree that even a protein
with a great deal of homology with another in the
database can not be identified.
Searching with Peptide Fingerprints
 A number of factors affect the utility of peptide fingerprinting.
The greater the experimental mass accuracy, the narrower you
can set your search tolerances, thereby increasing your
confidence in the match, and decreasing the number of "false
positive" responses.
 A common practice used to increase mass accuracy in peptide
fingerprinting is to employ an autolysis fragment from the
proteolytic enzyme as an internal standard to calibrate a
MALDI mass spectrum.
 Peptide fingerprinting is also amenable to the identification of proteins
in complex mixtures.
 Peptides generated from the digest of a protein mixture will simply
return two or more results that are a "good" fit.
 Peptides that are "left over" in a peptide fingerprint after the
identification of one component can be resubmitted for the
possible identification of another component.

Web addresses of some representative internet
resources for protein identification from mass
spectrometry data
Program
Web Address
BLAST
http://www.ebi.ac.uk/blastall/
Mascot
http://www.matrixscience.com/cgi/index.pl?page=/home.html
MassSearch
http://cbrg.inf.ethz.ch/Server/ServerBooklet/MassSearchEx.html
MOWSE
http://srs.hgmp.mrc.ac.uk/cgi-bin/mowse
PeptideSearch
http://www.narrador.emblheidelberg.de/GroupPages/PageLink/peptidesearchpage.html
Protein Prospector
http://prospector.ucsf.edu/
Prowl
http://prowl.rockefeller.edu/
SEQUEST
http://fields.scripps.edu/sequest/
Mascot
 Among the first programs for identifying proteins by peptide







mass fingerprinting, MOWSE, developed out of a collaboration
between Imperial Cancer Research Fund (ICRF) and SERC
Daresbury Laboratory, UK.
The name chosen was an acronym of Molecular Weight Search.
The MOWSE databases were fully indexed so as to allow very
rapid searching and retrieval of sequence data. Subsequently,
the software was further developed and renamed Mascot.
Licensed and distributed by Matrix Science Ltd.
Specialized tools include Peptide Mass Fingerprint, Sequence
Query, and MS/MS Ion Search.
Search output Web-based.
Good visual representation of search quality (graphical
probability chart).
Simple graphical user interface.
Reports MOWSE scores as a quantitative measure of search
quality.
Mowse Scoring
 Rather than just counting the number of matching peptides, Mowse uses





empirically determined factors to assign a statistical weight to each individual
peptide match. Rapid identification of proteins by peptide-mass
fingerprinting. Curr. Biol. 3:327, 1993.)
Scoring scheme assigns more weight to matches of higher molecular weight
peptides (more discriminating).
Compensates for the non-random distribution of fragment molecular weights
in proteins of different sizes.
Was first protein identification program to recognize that the relative
abundance of peptides of a given length in a proteolytic digest depends on
the lengths of both peptide and protein.
Developed for MALDI peptide mass fingerprinting.
Probability-Based Mowse
 Mascot incorporates a probability-based enhanced Mowse algorithm,
described in Perkins et al. (Probability-based protein identification by
searching sequence databases using mass spectrometry data.
Electrophoresis 20:3551-3567, 1999).
 A simple rule can be used to judge whether a result is significant or not.
Different types of matching (peptide masses and fragment ions) can be
combined in a single search.
Databases
 Three components are required for database searching support
of proteomics: MALDI or MS/MS data, the algorithms used to
search protein databases with the MALDI or MS/MS data, and
the protein databases themselves.
 The protein databases can be as small as one protein, can be
large, public domain databases of all known and predicted
proteins, or may be predicted open reading frames based on
genomic sequence.
 A major challenge for database searching is that these protein
databases are constantly changing, making database search
results potentially obsolete as new entries are added that better
fit the MALDI or MS data.
 Even as genomes are completed there is still flux as new coding
regions are identified and novel mechanisms of increased
translational complexity are better understood, such as
alternative splice products, RNA editing, and ribosome slippage
leading to novel, unexpected translation products.
Databases
 NCBI non-redundant (NCBInr)
Non-redundant database from the National Center for Biotechnology
Information for use with their search tools BLAST and Entrez; comprised of
translated sequences from the Genbank /EMBL/DDBJ consortium,
SwissProt, Protein Information Resource (PIR), and Brookhaven Protein
Data Bank (PDB).
 New releases are published bimonthly while updates occur daily.
 OWL
 OWL is comprised of Swiss-Prot, PIR, translated Genbank, and NRL-3D
(PDB). All sequences are compared to Swiss-Prot to remove identical and
“trivially different “ sequences. Has not been updated since May, 1999.
 SWISSPROT
 While SwissProt contains only a subset of proteins, the proteins in this
database are much better annotated and the sequences are much more
reliable than those available in any other database.
 MSDB
 Comprehensive, non-identical protein sequence database maintained by
the Proteomics Department at the Hammersmith Campus of Imperial
College London. Designed specifically for MS applications.

Databases
 EST Clusters (dBEST)





Division of GenBank that contains "single-pass" cDNA sequences, or
Expressed Sequence Tags (EST’s), from a number of organisms.
EST’s are relatively short, usually 3’ end sequences from isolated mRNA.
EST’s tend to be highly redundant and the sequence is much lower
quality than from other sources. An advantage to using these EST’s is
that they represent only expressed sequences (no introns) and include
alternative splice variants; their length, redundancy, and low quality are
far improved by using clustered EST’s, such as the Compugen clusters.
The EST database has some redundancy because it contains all possible
combinations of alternative splice products, and so it can be very large
(and slow to search).
During a Mascot search, the nucleic acid sequences are translated in all
six reading frames. dbEST is a very large database, and is divided into
three sections: EST_human, EST_mouse, and EST_others. Even so,
searches of these databases take far longer than a search of one of the
non-redundant protein databases. You should only search an EST
database if a search of a protein database has failed to find a match.
1000
all peaks are (M+H)+
1500
2000
*
2500
2719.48
*
2476.21
2550.52
2005.07
*trypsin autolysis
1811.85
1849.12
1375.76
1424.85
1505.77
1574.20
1665.89
1287.73
1247.70
1116.67
MALDI-MS peptide fingerprint
(tryptic digest of a single protein)
3000
m/z
Mascot (Matrix Science) for peptide mass
fingerprints
enter peak list
Mascot (Matrix Science) for peptide mass
fingerprints
possible identification
Mascot (Matrix Science) for peptide mass
fingerprints
get more info on probable proteins
list of all possible matches
Mascot (Matrix Science) for peptide mass
fingerprints
Mascot (Matrix Science) for peptide mass
fingerprints
tryptic peptides
that matched
peptides that
did not match
Mascot (Matrix Science) for peptide mass
fingerprints
tryptic peptides in protein sequence
better mass accuracy
improves identification
process
LC-MS/MS for protein identification
 To provide further confirmation of the identification, if a tandem mass
spectrometer (MS/MS) is available, peptide ions can be dissociated in
the mass spectrometer to provide direct sequence information. Product
ions from an MS/MS spectrum can be compared to available
sequences using powerful software toolsl.
 For a single sample, LC-MS/MS analysis included two discrete steps:
(a) LC-MS peptide mapping to identify peptide ions from the digestion
mixture and to deduce their molecular weights, and (b) LC-MS/MS of
the previously detected peptides to obtain sequence information for
protein identification.
Automated LC-MS/MS and database
searching
 Current mass spectral technology permits the generation of
MS/MS data at an unprecedented rate. Prior to the generation
of powerful computer-based database searching strategies, the
largest bottleneck in protein identification was the manual
interpretation of this MS/MS data to extract the sequence
information. Today, many computer-based search strategies
that employ MS/MS data require no operator interpretation at all.
 Analogous to the approach described for peptide fingerprinting,
these programs take the individual protein entries in a database
and electronically "digest" them to generate a list of theoretical
peptides for each protein.
 However, in the use of MS/MS data, these theoretical
peptides are further manipulated to generate a second level
of lists which contain theoretical fragment ion masses that
would be generated in the MS/MS experiment for each
theoretical peptide.
Automated LC-MS/MS and database
searching
 These programs simply compare the list of experimentally
determined fragment ion masses from the MS/MS experiment of
the peptide of interest with the theoretical fragment ion masses
generated by the computer program.
 The recent advent of data-dependant scanning functions has
permitted the unattended acquisition of MS/MS data. An
example of a raw MS/MS data searching program that takes
particular advantage of this ability is SEQUEST.




SEQUEST will input the data from a data-dependant LC/MS
chromatogram and automatically strip out all of the MS/MS
information for each individual peak, and submit it for database
searching using the strategy discussed above.
Each peak is treated as a separate data file, making it especially
useful for the on-line separation and identification of individual
components in a protein mixture.
SEQUEST cross-correlates uninterpreted MS/MS mass spectra of
peptides from protein/nucleotide databases. The software can
analyze a single spectrum or an entire LC-MS/MS peptide map.
No user interpretation of MS/MS spectra is involved.
Theoretical
Peptide
Theoretical Fragment
Masses
LPNLIYHR
Seq
L
P
N
L
I
Y
H
R
Match?
Proteolytic Digest
#
1
2
3
4
5
6
7
8
B
114.1
211.1
325.2
438.3
551.3
714.4
851.5
1007.6
Y
1025.6
912.5
815.4
701.4
588.3
475.2
312.2
175.1
#
8
7
6
5
4
3
2
1
MS/MS
100
Experimental
Fragment Masses
41.63
HPLC-MS
475.3
100
588.3
456.7
54.28
50
60.16
62.59
38.27
29.02
0
25
30
701.3
49.20
46.75
410.3
33.59
35
325.2
50
851.5
912.5
212.1
40
45
Time (min)
50
55
60
200
300
400
815.4
500
600
m/z
700
800
900 1000
Direct identification of proteins
using mass spectrometry  Removes the requirement to separate





proteins by electrophoresis, etc
MudPIT: multidimensional protein
identification technology, or “Shotgun”
approach
Protein lysate is digested with trypsin
The peptide mixture is loaded onto a
strong cation exchange (SCX) column (to
separate on the basis of charge). A
discrete fraction of peptides is displaced
from the SCX column using a salt step
gradient to a reversed-phase (RP) column
(to separate on the basis of
hydrophobicity).
This fraction is eluted from the RP column
into the MS. This iterative process is
repeated, obtaining the fragmentation
patterns of peptides in the original peptide
mixture.
MS/MS spectra are used to identify the
proteins in the original protein complex.
Link et al. Nature Biotechnology 17, 676 (1999)
Large-scale analysis of the yeast
proteome by MudPIT
 Yates and coworkers, Nature




Biotech. (2001) 19, 242-247
Assigned 5,540 peptides to MS
spectra leading to the identification
of 1,484 proteins from the S.
cerevisiae proteome
Of 6,216 ORFs in yeast genome,
83% have CAI values between 0
and 0.20 (i.e., predicted to be
present at low levels) (Fig. A)
MudPIT data: 791 or 53.3% of the
proteins identified have a CAI of
<0.2 (1.7 peptides per protein) (Fig.
B)
Number of peptides per protein
increases with increasing CAI (Fig.
C)
Approaches for Protein Sequencing and
Identification
“Top Down”
MS/MS
MIRERICACVLALGMLTGFTHAFGSKDAAADGKPLVVTTIGMIADAVKNIAQGDVHLKGLMGP
GVDPHLYTATAGDVEWLGNADLILYNGLHLETKMGEVFSKLRGSRLVVAVSETIPVSQRLSLE
EAEFDPHVWFDVKLWSYSVKAVYESLCKLLPGKTREFTQRYQAYQQQLDKLDAYVRRKAQS
LPAERRVLVTAHDAFGYFSRAYGFEVKGLQGVSTASEASAHDMQELAAFIAQRKLPAIFIESSI
PHKNVEALRDAVQARGHVVQIGGELFSDAMGDAGTSEGTYVGMVTHNIDTIVAALAR
The molecular mass of an intact protein defines the native covalent state of a
gene’s product, including the effects of post-transcriptional/translational
modifications, and associated heterogeneity, that are modulated by the actions of
other gene products . Moreover, the fragmentation pattern from large proteins
can generate sufficient information for identification from sequence databases,
particularly when combined with accurate mass measurements of both the intact
molecule and its product ions.
In-Source Decay (ISD) for
Protein Sequencing
 Peptides and large proteins can be
fragmented by ISD
 Fragmentation occurs in the MALDI
ion source
 Complete sequence
 not generally well controlled
information not present, but
 Reflectron TOF not necessary
extensive stretches of
(linear TOF sufficient to measure
sequence from the N- and/or
product ions
C-termini observed
cut
P
E
P
E
P
P
E
P
T
D
P
E
P
T
I
M
P
E
P
T
I
D
P
E
P
T
I
D
P
T
I
F
R
E
A
G
...TIDE...
E
T
N
E
MALDI-ISD-TOF Mass Spectrometry of
Proteins
Sequence Information
(In-Source Decay)
Protein 1
Molecular Weight
Information
Protein 2
5000
10000
15000
m/z
20000
25000
MALDI-ISD-TOF Mass Spectrometry of
Proteins
 ISD generally yields c-ions or z-ions
Sequence information from the N-terminus
L
A
Y
G G
E
G
F
E
D
H
R
L
K/Q
E
D
T
L
A
F
2500
G
D
E
G
3000
F
E
m/z
D
H
3500
R
V
A
F
L/N
4000
D
PW?
WP?
Top-down sequencing of transferrin by
ESI-MS/MS
(top)
ESI-QqTOF-MS
of
transferrin and (bottom) ESIMS/MS of 36+ charged
molecule. Sequence specific
bn-products from residues 5669 are generated. In addition,
a series of larger products
appears at higher m/z above
the
precursor
molecule
position that range in size
from 69-73 kDa that are
consistent
for
the
yncomplement to the bnproducts observed in the
lower m/z region of the
spectrum. (Thevis et al, J.
Am. Soc. Mass Spectrom.
2003, 14, 635).
Masses and compositions of commonly occuring amino
acid residues